I haven't had it happen before, but just today while I was in puzzle longer than usual because I thought I had found an example of a "multiple solution" puzzle and was doing screen captures to post the puzzle, at one point I was marking X's in the puzzle when suddenly this survey appeared in the puzzle area. I didn't want to click on the survey and I couldn't see how to close it, so I ended up hitting the Refresh page, which gave me the puzzle back, but all cleared. If you look at the URL, there is "&clear=true" at the end, so perhaps if I had removed that, I could have gotten the puzzle back with out it being cleared.
This is a work computer, so I don't have an option of upgrading or installing a different browser. This happens to be IE8. As it is a work computer, firewall, and virus protection is in full force, so I do think it is a "legititmate" ad.

Of course the puzzle itself wasn't multi-solution. After going through it for the eighth time doing screen shots of the "possible different solutions", I found a simple X off that I had missed every previous pass through the clues, and with that one in place, the proper solution was quickly resolved.

p.s. Happened again, Dec. 2nd, after my first X on the first puzzle of the month.

I noticed in a few puzzles I was doing, that after I had cleared the grid to restart the game, some words in the clues were highlighted in blue. If my mouse rested on one of the highlighted words, a pop up ad comes up. It blocks the clues from view. I tried closing it with the x on the ad to no avail. If I click on the pop up it will bring me to some website.
If I try to clear the grid again, the puzzle comes up with no entries, but the ad was still showing. I had to start a new game to remove it.
As a newbie somewhat to logic puzzles, I do have to clear the grid a few times before I solve it and that is usually when it happens. Never got it on the new puzzles. Very annoying whatever it is.

The sort of "in-text" links you're describing are something we absolutely don't use on this site - if they are appearing for you, it is most likely as a result of some sort of adware/spyware that is attached to your browser. You may want to run an anti-spyware program to detect and remove this (I usually recommend "Malware Bytes", which is free).